add neighbor list kind output to screen

Merge pull request #349 from akohlmey/collected-small-fixes
collected fixes and improvements
2017-01-20 13:24:09 -07:00 · 2017-01-20 13:19:43 -07:00 · 2017-01-20 13:15:16 -07:00 · 2017-01-20 13:14:59 -07:00 · 2017-01-20 14:30:46 -05:00 · 2017-01-19 20:47:10 -05:00
331 changed files with 1178 additions and 309 deletions
--- a/.gitignore
+++ b/.gitignore
@ -0,0 +1,34 @@
+*~
+*.o
+*.so
+*.cu_o
+*.ptx
+*_ptx.h
+*.a
+*.d
+*.x
+*.exe
+*.dll
+*.pyc
+__pycache__
+
+Obj_*
+log.lammps
+log.cite
+*.bz2
+*.gz
+*.tar
+.*.swp
+*.orig
+*.rej
+.vagrant
+\#*#
+.#*
+
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
--- a/doc/.gitignore
+++ b/doc/.gitignore
@ -0,0 +1,5 @@
+/html
+/LAMMPS.epub
+/LAMMPS.mobi
+/Manual.pdf
+/Developer.pdf
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="26 Jan 2017 version">
+<META NAME="docnumber" CONTENT="20 Jan 2017 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@ -21,7 +21,7 @@
 <H1></H1>

 LAMMPS Documentation :c,h3
-26 Jan 2017 version :c,h4
+20 Jan 2017 version :c,h4

 Version info: :h4

--- a/doc/src/compute_temp_asphere.txt
+++ b/doc/src/compute_temp_asphere.txt
--- a/doc/src/compute_temp_body.txt
+++ b/doc/src/compute_temp_body.txt
--- a/doc/src/compute_temp_sphere.txt
+++ b/doc/src/compute_temp_sphere.txt
--- a/doc/src/fix_bond_break.txt
+++ b/doc/src/fix_bond_break.txt
--- a/doc/src/fix_bond_create.txt
+++ b/doc/src/fix_bond_create.txt
--- a/doc/src/fix_bond_swap.txt
+++ b/doc/src/fix_bond_swap.txt
--- a/doc/src/fix_lb_fluid.txt
+++ b/doc/src/fix_lb_fluid.txt
--- a/doc/src/fix_lb_momentum.txt
+++ b/doc/src/fix_lb_momentum.txt
--- a/doc/src/fix_lb_pc.txt
+++ b/doc/src/fix_lb_pc.txt
--- a/doc/src/fix_lb_rigid_pc_sphere.txt
+++ b/doc/src/fix_lb_rigid_pc_sphere.txt
--- a/doc/src/fix_lb_viscous.txt
+++ b/doc/src/fix_lb_viscous.txt
--- a/doc/src/fix_nph_asphere.txt
+++ b/doc/src/fix_nph_asphere.txt
--- a/doc/src/fix_nph_body.txt
+++ b/doc/src/fix_nph_body.txt
--- a/doc/src/fix_nph_sphere.txt
+++ b/doc/src/fix_nph_sphere.txt
--- a/doc/src/fix_npt_asphere.txt
+++ b/doc/src/fix_npt_asphere.txt
--- a/doc/src/fix_npt_body.txt
+++ b/doc/src/fix_npt_body.txt
--- a/doc/src/fix_npt_sphere.txt
+++ b/doc/src/fix_npt_sphere.txt
--- a/doc/src/fix_nve_asphere.txt
+++ b/doc/src/fix_nve_asphere.txt
--- a/doc/src/fix_nve_asphere_noforce.txt
+++ b/doc/src/fix_nve_asphere_noforce.txt
--- a/doc/src/fix_nve_body.txt
+++ b/doc/src/fix_nve_body.txt
--- a/doc/src/fix_nve_line.txt
+++ b/doc/src/fix_nve_line.txt
--- a/doc/src/fix_nve_sphere.txt
+++ b/doc/src/fix_nve_sphere.txt
--- a/doc/src/fix_nve_tri.txt
+++ b/doc/src/fix_nve_tri.txt
--- a/doc/src/fix_nvt_asphere.txt
+++ b/doc/src/fix_nvt_asphere.txt
--- a/doc/src/fix_nvt_body.txt
+++ b/doc/src/fix_nvt_body.txt
--- a/doc/src/fix_nvt_sphere.txt
+++ b/doc/src/fix_nvt_sphere.txt
--- a/doc/src/fix_ti_spring.txt
+++ b/doc/src/fix_ti_spring.txt
--- a/doc/src/min_style.txt
+++ b/doc/src/min_style.txt
--- a/doc/src/pair_dipole.txt
+++ b/doc/src/pair_dipole.txt
--- a/doc/src/pair_gayberne.txt
+++ b/doc/src/pair_gayberne.txt
--- a/doc/src/pair_resquared.txt
+++ b/doc/src/pair_resquared.txt
--- a/doc/src/pair_smtbq.txt
+++ b/doc/src/pair_smtbq.txt
--- a/doc/utils/converters/.gitignore
+++ b/doc/utils/converters/.gitignore
@ -1,2 +1 @@
-__pycache__
 *.egg-info
--- a/examples/COUPLE/fortran2/.gitignore
+++ b/examples/COUPLE/fortran2/.gitignore
@ -0,0 +1 @@
+*.mod
--- a/examples/USER/misc/ti/in.ti_spring
+++ b/examples/USER/misc/ti/in.ti_spring
--- a/examples/mscg/output_9Jan17/log.lammps
+++ b/examples/mscg/output_9Jan17/log.lammps
@ -1,140 +0,0 @@
-LAMMPS (4 Nov 2016)
-units real
-atom_style full
-pair_style zero 10.0
-
-read_data data.meoh
-  orthogonal box = (-20.6917 -20.6917 -20.6917) to (20.6917 20.6917 20.6917)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  1000 atoms
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-pair_coeff * *
-
-thermo 1
-thermo_style custom step
-
-# Test 1a: range finder functionality
-fix 1 all mscg 1 range on
-rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
-Neighbor list info ...
-  1 neighbor list requests
-  update every 1 steps, delay 10 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 12
-  ghost atom cutoff = 12
-  binsize = 6 -> bins = 7 7 7
-Memory usage per processor = 5.44227 Mbytes
-Step 
-       0 
-     250 
-     500 
-     750 
-    1000 
-    1250 
-    1500 
-    1750 
-    2000 
-    2250 
-    2500 
-    2750 
-    3000 
-    3250 
-    3500 
-    3750 
-    4000 
-    4250 
-    4500 
-Loop time of 0.695789 on 1 procs for 19 steps with 1000 atoms
-
-Performance: 2.359 ns/day, 10.172 hours/ns, 27.307 timesteps/s
-92.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
-Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Bond    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0          | 0          | 0          |   0.0 |  0.00
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 0.6958     |            |       |100.00
-
-Nlocal:    1000 ave 1000 max 1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    2934 ave 2934 max 2934 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    50654 ave 50654 max 50654 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 50654
-Ave neighs/atom = 50.654
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-print "TEST_1a mscg range finder"
-TEST_1a mscg range finder
-unfix 1
-
-# Test 1b: force matching functionality
-fix 1 all mscg 1
-rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
-Memory usage per processor = 5.44227 Mbytes
-Step 
-       0 
-     250 
-     500 
-     750 
-    1000 
-    1250 
-    1500 
-    1750 
-    2000 
-    2250 
-    2500 
-    2750 
-    3000 
-    3250 
-    3500 
-    3750 
-    4000 
-    4250 
-    4500 
-Loop time of 1.48638 on 1 procs for 19 steps with 1000 atoms
-
-Performance: 1.104 ns/day, 21.731 hours/ns, 12.783 timesteps/s
-88.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
-Pair    | 0          | 0          | 0          |   0.0 |  0.00
-Bond    | 0          | 0          | 0          |   0.0 |  0.00
-Neigh   | 0          | 0          | 0          |   0.0 |  0.00
-Comm    | 0          | 0          | 0          |   0.0 |  0.00
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 1.486      |            |       |100.00
-
-Nlocal:    1000 ave 1000 max 1000 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    2934 ave 2934 max 2934 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    50654 ave 50654 max 50654 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 50654
-Ave neighs/atom = 50.654
-Ave special neighs/atom = 0
-Neighbor list builds = 0
-Dangerous builds = 0
-print "TEST_1b mscg force matching"
-TEST_1b mscg force matching
-
-print TEST_DONE
-TEST_DONE
-Total wall time: 0:00:02
--- a/examples/vashishta/InP.vashishta
+++ b/examples/vashishta/InP.vashishta
--- a/examples/vashishta/SiO.1990.vashishta
+++ b/examples/vashishta/SiO.1990.vashishta
--- a/lib/.gitignore
+++ b/lib/.gitignore
@ -0,0 +1 @@
+Makefile.lammps
--- a/lib/gpu/cudpp_mini/cudpp.h
+++ b/lib/gpu/cudpp_mini/cudpp.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // CUDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt in
 // the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_globals.h
+++ b/lib/gpu/cudpp_mini/cudpp_globals.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt in
 // the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_maximal_launch.h
+++ b/lib/gpu/cudpp_mini/cudpp_maximal_launch.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_plan.h
+++ b/lib/gpu/cudpp_mini/cudpp_plan.h
@ -2,7 +2,7 @@
 // CUDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
 // $Revision: 3572$
-// $Date$
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_plan_manager.h
+++ b/lib/gpu/cudpp_mini/cudpp_plan_manager.h
@ -2,7 +2,7 @@
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
 // $Revision: 3572$
-// $Date$
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_radixsort.h
+++ b/lib/gpu/cudpp_mini/cudpp_radixsort.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_scan.h
+++ b/lib/gpu/cudpp_mini/cudpp_scan.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt 
 // in the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/cudpp_util.h
+++ b/lib/gpu/cudpp_mini/cudpp_util.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt in
 // the root directory of this source distribution.
--- a/lib/gpu/cudpp_mini/sharedmem.h
+++ b/lib/gpu/cudpp_mini/sharedmem.h
@ -1,8 +1,8 @@
 // -------------------------------------------------------------
 // cuDPP -- CUDA Data Parallel Primitives library
 // -------------------------------------------------------------
-// $Revision$
-// $Date$
+// $Revision: 5289 $
+// $Date: 2010-11-23 13:04:43 -0700 (Tue, 23 Nov 2010) $
 // ------------------------------------------------------------- 
 // This source code is distributed under the terms of license.txt 
 // in the root directory of this source distribution.
--- a/lib/kokkos/.gitignore
+++ b/lib/kokkos/.gitignore
@ -1,8 +0,0 @@
-# Standard ignores
-*~
-*.pyc
-\#*#
-.#*
-.*.swp
-.cproject
-.project
--- a/lib/kokkos/config/configure_compton_cpu.sh
+++ b/lib/kokkos/config/configure_compton_cpu.sh
--- a/lib/kokkos/config/configure_compton_mic.sh
+++ b/lib/kokkos/config/configure_compton_mic.sh
--- a/lib/kokkos/config/configure_kokkos.sh
+++ b/lib/kokkos/config/configure_kokkos.sh
--- a/lib/kokkos/config/configure_kokkos_nvidia.sh
+++ b/lib/kokkos/config/configure_kokkos_nvidia.sh
--- a/lib/kokkos/config/configure_shannon.sh
+++ b/lib/kokkos/config/configure_shannon.sh
--- a/lib/linalg/Makefile.gfortran
+++ b/lib/linalg/Makefile.gfortran
--- a/lib/linalg/Makefile.mingw32-cross
+++ b/lib/linalg/Makefile.mingw32-cross
--- a/lib/linalg/Makefile.mingw64-cross
+++ b/lib/linalg/Makefile.mingw64-cross
--- a/lib/meam/.gitignore
+++ b/lib/meam/.gitignore
@ -0,0 +1 @@
+*.mod
--- a/lib/meam/Makefile.tbird
+++ b/lib/meam/Makefile.tbird
--- a/lib/meam/meam_data.F
+++ b/lib/meam/meam_data.F
--- a/lib/meam/meam_dens_final.F
+++ b/lib/meam/meam_dens_final.F
--- a/lib/meam/meam_dens_init.F
+++ b/lib/meam/meam_dens_init.F
--- a/lib/meam/meam_force.F
+++ b/lib/meam/meam_force.F
--- a/lib/meam/meam_setup_done.F
+++ b/lib/meam/meam_setup_done.F
--- a/lib/meam/meam_setup_global.F
+++ b/lib/meam/meam_setup_global.F
--- a/lib/meam/meam_setup_param.F
+++ b/lib/meam/meam_setup_param.F
--- a/lib/reax/Makefile.g95
+++ b/lib/reax/Makefile.g95
--- a/lib/reax/Makefile.gfortran
+++ b/lib/reax/Makefile.gfortran
--- a/potentials/WL.meam
+++ b/potentials/WL.meam
@ -1,13 +0,0 @@
-# DATE: 2017-01-25 CONTRIBUTOR: Aidan Thompson, athomps@sandia.gov,  CITATION: Lee, Baskes, Kim, Cho. Phys. Rev. B, 64, 184102 (2001) 
-rc = 3.8
-delr = 0.1
-augt1 = 0
-erose_form = 2
-zbl(1,1) = 0
-nn2(1,1) = 1
-Ec(1,1) = 8.66
-re(1,1) = 2.74
-attrac(1,1) = 0
-repuls(1,1) = 0
-Cmin(1,1,1) = 0.49
-Cmax(1,1,1) = 2.8
--- a/python/.gitignore
+++ b/python/.gitignore
@ -1,3 +1 @@
-*.pyc
-__pycache__
-build
+/build
--- a/python/examples/pylammps/.gitignore
+++ b/python/examples/pylammps/.gitignore
@ -0,0 +1 @@
+*.orig
--- a/src/.gitignore
+++ b/src/.gitignore
--- a/src/ASPHERE/compute_temp_asphere.cpp
+++ b/src/ASPHERE/compute_temp_asphere.cpp
--- a/src/ASPHERE/compute_temp_asphere.h
+++ b/src/ASPHERE/compute_temp_asphere.h
--- a/src/ASPHERE/fix_npt_asphere.cpp
+++ b/src/ASPHERE/fix_npt_asphere.cpp
--- a/src/ASPHERE/fix_npt_asphere.h
+++ b/src/ASPHERE/fix_npt_asphere.h
--- a/src/ASPHERE/fix_nve_asphere.cpp
+++ b/src/ASPHERE/fix_nve_asphere.cpp
--- a/src/ASPHERE/fix_nve_asphere.h
+++ b/src/ASPHERE/fix_nve_asphere.h
--- a/src/ASPHERE/fix_nve_asphere_noforce.h
+++ b/src/ASPHERE/fix_nve_asphere_noforce.h
--- a/src/ASPHERE/fix_nvt_asphere.cpp
+++ b/src/ASPHERE/fix_nvt_asphere.cpp
--- a/src/ASPHERE/fix_nvt_asphere.h
+++ b/src/ASPHERE/fix_nvt_asphere.h
--- a/src/ASPHERE/pair_gayberne.cpp
+++ b/src/ASPHERE/pair_gayberne.cpp
--- a/src/ASPHERE/pair_gayberne.h
+++ b/src/ASPHERE/pair_gayberne.h
--- a/src/ASPHERE/pair_resquared.cpp
+++ b/src/ASPHERE/pair_resquared.cpp
--- a/src/ASPHERE/pair_resquared.h
+++ b/src/ASPHERE/pair_resquared.h
--- a/src/BODY/compute_temp_body.cpp
+++ b/src/BODY/compute_temp_body.cpp
--- a/src/BODY/compute_temp_body.h
+++ b/src/BODY/compute_temp_body.h
--- a/src/BODY/fix_npt_body.cpp
+++ b/src/BODY/fix_npt_body.cpp
--- a/src/BODY/fix_npt_body.h
+++ b/src/BODY/fix_npt_body.h
--- a/src/BODY/fix_nvt_body.cpp
+++ b/src/BODY/fix_nvt_body.cpp
--- a/src/BODY/fix_nvt_body.h
+++ b/src/BODY/fix_nvt_body.h
--- a/src/COLLOID/pair_brownian.cpp
+++ b/src/COLLOID/pair_brownian.cpp
--- a/src/COLLOID/pair_lubricate.cpp
+++ b/src/COLLOID/pair_lubricate.cpp
--- a/src/DIPOLE/pair_lj_cut_dipole_cut.cpp
+++ b/src/DIPOLE/pair_lj_cut_dipole_cut.cpp
--- a/src/DIPOLE/pair_lj_cut_dipole_cut.h
+++ b/src/DIPOLE/pair_lj_cut_dipole_cut.h
--- a/src/DIPOLE/pair_lj_cut_dipole_long.cpp
+++ b/src/DIPOLE/pair_lj_cut_dipole_long.cpp
--- a/src/DIPOLE/pair_lj_cut_dipole_long.h
+++ b/src/DIPOLE/pair_lj_cut_dipole_long.h
--- a/Show More
+++ b/Show More